Reanalysis RNA-Seq (GSE147507)

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Summary of Data/ Analysis

  • 20 Samples total
  • source cell lines - A549 ( Lung Adenocarcinoma), NHBE ( Primary Human Bronchial Lung Epithelium Cells )
  • Raw Fastq Downloaded from GEO:GSE147507
  • Aligned to hg38 using STAR
  • Raw Counts using HTSeq
  • Normalized Expression FPKM

Infected with 3 strains:

  • SARS-Cov2 - US/WA1 Strain
  • Respiratory syncytial virus(RSV)
  • Influenza A (IAV)

Multiplicity of infection (MOI) variables - [ ratio of virions to target cells ]

  • SAR-Cov2 in NHBE - MOI 2.0
  • SAR-Cov2 in A549 - MOI 0.2
  • RSV in A549 - MOI 15
  • IAV in A549 - MOI 5

Differential Expression

  • A549 : SARS-CoV2 (MOI 0.2) vs. Cov2-Mock
  • NHBE : SARS-CoV2 (MOI 2) vs. Cov2-Mock

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Sample Annotation

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Principle Component Analysis

QC Genes

A549 Comparisons

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Differential Expression Analysis

  • Using Limma with voom transformation
  • A549 SARS_CoV2 vs. Mock_Cov2
  • N = 175 significantly changed genes with cut off FDR < 0.05

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Heatmap A549 - Sars_Cov2

Volcano Plot - Sars_Cov2 A549

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DE Stats all genes (A549 SARS_CoV2 vs. Mock_Cov2)

Significanty Upregulated in SAR-CoV2-A549 ( FDR < 0.05)

Significanty Downregulated in SAR-CoV2-A549 ( FDR < 0.05) (A549 SARS_CoV2 vs. Mock_Cov2)

A549 - Pathways

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Pathway analysis summary

GSEA Pathway analysis perforemd on A549 ( MOI 0.2 ) SARS-Cov2 vs. SARS2-Cov2-Mock

  • Using the Following Databses:

    • KEGG (Version 6.2 msigDB)
    • REACTOME (Version 6.2 msigDB )
    • GO Biological Processes (Version 7 msigDB)
  • FDR < 0.25

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KEGG Significanty Enriched Pathway Up in A549-SARS_Cov2 ( FDR < 0.25)

KEGG Significanty Enriched Pathway Down in A549-SARS_Cov2 ( FDR < 0.25)

REACTOME - Significanty Enriched Pathway Up in A549-SARS_Cov2 ( FDR < 0.25)

REACTOME - Significanty Enriched Pathway Down in A549-SARS_Cov2 ( FDR < 0.25)

GO Pathways - Significanty Enriched Pathway Up in A549-SARS_Cov2 ( FDR < 0.25)

GO Pathways - Significanty Enriched Pathway Down in A549-SARS_Cov2 ( FDR < 0.25)

NHBE Comparisons

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Differential Expression Analysis

  • Using Limma with voom transformation
  • SARS_Cov2 NHBE vs. SARS CoV2 MOCK
  • N= 252 Signficantly Genes with cut off FDR < 0.05

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Heatmap NHBE - Sars_Cov2

Volcano Plot - Sars_Cov2 NHBE

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DE Stats all genes ( NHBE SARS_CoV2 vs. Mock_Cov2)

Significanty Upregulated genes in SAR-CoV2 NHBE (FDR < 0.05) ( NHBE SARS_CoV2 vs. Mock_Cov2)

Significanty Downregulated genes in SAR-CoV2 NHBE( N=180, FDR < 0.05) ( NHBE SARS_CoV2 vs. Mock_Cov2)

NHBE - Pathways

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Pathway analysis summary

GSEA Pathway analysis perforemd on NHBE SARS-Cov2 ( MOI 2) vs. SARS2-Cov2-Mock

  • Using the Following Databses:

    • KEGG (Version 6.2 msigDB)
    • REACTOME (Version 6.2 msigDB )
    • GO Biological Processes (Version 7 msigDB)
  • FDR < 0.25

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KEGG Significanty Enriched Pathway Up in NHBE-SARS_Cov2 ( FDR < 0.25)

KEGG Significanty Enriched Pathway Down in NHBE-SARS_Cov2 ( FDR < 0.25)

REACTOME Significanty Enriched Pathway Up in NHBE-SARS_Cov2 ( FDR < 0.25)

REACTOME Significanty Enriched Pathway Down in NHBE-SARS_Cov2 ( FDR < 0.25)

GO Pathways - Significanty Enriched Pathway Up in NHBE-SARS_Cov2 ( FDR < 0.25)

GO Pathways - Significanty Enriched Pathway Down in NHBE-SARS_Cov2 ( FDR < 0.25)

Overlapping Gene Changes

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Comparing Genes between A549 and NHBE - Sars-Cov2

Analyzed using GeneOverlap

Analyzed using GeneOverlap

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List of Shared Upregulated Genes

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Heatmap Overlapping Genes in NHBE & A549 - Sars_Cov2